[Bioc-devel] rsvg on mac

Wed Feb 14 02:24:17 CET 2018

Hi Kevin,

As Val said, some CRAN packages with native code won't compile
on our Windows or Mac builders because of missing components,
and rsvg is one of them. Please keep in mind that we already
install many external components required for the compilation
of Bioconductor packages. The process of doing so on a fresh
Mac El Capitan system is documented here:

https://github.com/Bioconductor/BBS/blob/master/Doc/Prepare-MacOSX-El-Capitan-HOWTO.TXT

Installing these components is time consuming and there is always
the risk to introduce some conflicts/instabilities when installing
new components. Given that our resources are limited, it wouldn't
make much sense that we do this for those CRAN packages for which
the binaries are only temporarily unavailable.

Cheers,
H.

On 02/13/2018 12:56 PM, Kevin Horan wrote:
> Valerie,
> 
>       Ok, I understand the difference now. Would it be possible to
> install the system requirement for rsvg ( just on devel)?
> 
>       I'm trying to generate plots in either PNG or SVG with OpenBabel.
> For PNG, OpenBabel requires it's own Cario library be installed on the
> system (doesn't seem to work with what is built into R, as it needs to
> be linked with OpenBabel). I've not been successful getting the Cairo
> lib installed on windows, but using SVG with OpenBabel, and then reading
> that back into R with rsvg, works fine. So it seems I'll need a extra
> system library either way ( either Cairo, or librsvg2).
> 
> Thanks.
> 
> Kevin
> 
> 
> On 02/13/2018 06:43 AM, Obenchain, Valerie wrote:
>> Hi,
>>
>> By default, the build system installs CRAN dependencies on the Mac and
>> Windows builders with 'type=both':
>>
>>    install.packages("mypackage", type="both")
>>
>> This means it first tries to install the binary and if that fails, it
>> tries to install from source. Packages without native code or
>> SystemRequirements usually install fine from source. This is the case
>> for DiagrammeR which can be installed on the build machines. rsvg is
>> in the Suggests field of DiagrammeR so rsvg is not needed to install
>> or load the package.
>>
>> The rsvg package is different in that it has 'librsvg2' as a
>> SystemRequirement which is not installed on the Mac (or Windows) build
>> machine:
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_rsvg_index.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs&s=ykWNmVUAiB_w-DbtSqe1v5yWUnT_KpcxPCqUSLt873w&e=
>>
>> We do install all SystemRequirements for Bioconductor packages on the
>> Mac and Windows builders but not for CRAN packages. Installing all
>> third party requirements of CRAN dependencies would add significantly
>> to the build system maintenance and really only serves a purpose in
>> this window of time where binaries are not available for devel.
>>
>> cc'ing Herve in case he has more to add.
>>
>>
>> Valerie
>>
>>
>>
>>
>> On 02/12/2018 12:25 PM, Kevin Horan wrote:
>>> Valerie,
>>>      I'm not sure I understand. I looked at another package that is
>>> currently installed on the mac devel machine, DiagrammeR
>>> (https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_package-3DDiagrammeR&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs&s=7UDK9omF9qsdLzWH6wEh_fyNE5BuQbNbJzc0v925ElE&e=), and it has the same
>>> set of links on the CRAN site as rsvg does. In particular, it does
>>> not show a  r-devel version for El Capitan.
>>>      Also, rsvg is not installed on the release mac build machine
>>> either, which it should have a version for.
>>>
>>> Kevin
>>>
>>> On 02/07/2018 09:09 AM, Obenchain, Valerie wrote:
>>>> Hi Kevin,
>>>>
>>>> CRAN binaries for El Capitan in devel aren't available. You can see
>>>> this on the rsvg landing page:
>>>>
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_rsvg_index.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs&s=ykWNmVUAiB_w-DbtSqe1v5yWUnT_KpcxPCqUSLt873w&e=
>>>>
>>>> Nothing we can do until CRAN makes them available.
>>>>
>>>> Valerie
>>>>
>>>>
>>>> On 02/07/2018 08:29 AM, Kevin Horan wrote:
>>>>> The ChemmineR build is failing on the mac due to a new dependency not
>>>>> being available, the package "rsvg". Would it be possible to install
>>>>> that on the mac build machine? Thanks.
>>>>>
>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ChemmineR_merida2-2Dinstall.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs&s=B43U-waIixUyD4yJS4OySSIX5jVaAXp98jUM348m8oU&e=
>>>>>
>>>>>
>>>>> Kevin
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org  mailing list
>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=y_AVoDJvCaCexHFznr_ua93-DoFexhIDSKUK1NcBzNs&s=PprBTJthrOIxSMiD9GCrT3UpvPflkGUmM65M7FDTevs&e=
>>>>>
>>>>
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-- 
Hervé Pagès

Program in Computational Biology
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